Abstract: Methods for making synthetic gene clusters are described.

Abstract: The invention relates to systems and methods for production of compounds by yeast and other organisms. In one approach yeast engineered for production of a compound of commercial value is cultured together with a cellulosic bacteria, and the yeast uses a metabolic product produced by the bacteria as a carbon source. Methyl halides are an example of compounds that may be produced by this process. The invention also relates to production of organic compounds using genetically engineered organisms expressing a S-adenosylmethionine (SAM)-dependent methyl halide transferase. In one approach the organism, halides and a carbon source are incubated in a cultivation medium under conditions in which methyl halide is produced. The methyl halide may be collected and converted into non-halogenated organic molecules.

Abstract: An apparatus with an oscillating circuit, which is excitable by means of an alternating signal source. The oscillating circuit includes a non-linear circuit element. The apparatus is designed so that the non-linear circuit element is operable in a non-linear operating range and with a frequency above its limiting frequency.

Abstract: Methods for making synthetic gene clusters are described.

Abstract: Expression cassettes comprising promoter and terminator combinations are provided and can be used to tune gene expression. Synthetic yeast promoters and methods of making them also are provided.

Abstract: Aspects of the invention relate to a regulatory system that follows design principles of natural systems but creates novel synthetic biology tools using bisected polymerase proteins.

Abstract: The invention relates to methods and products for generating diverse libraries of genetic material. The products include libraries and constructed nucleic acids as well as kits and databases and systems thereof.

Abstract: The invention relates to DNA destruction devices and related methods reagents and kits. The DNA destruction devices are useful for achieving target specific DNA destruction in vivo using a system that involves an actuator element and a CRISPR array, under specific regulatory control.

Abstract: Cells that can synthesize oligonucleotides in vivo to produce a nucleic acid nanostructure are described. Methods for producing oligonucleotide nanostructures for use in regulating gene expression and altering biological pathways are provided. Methods of performing multiplex automated genome editing (MAGE) are also provided.

Abstract: Disclosed is a process in which a recombinant organism, such as a yeast, expressing a heterologous S-adenosylmethionine (SAM)-dependent methyl halide transferase (MHT) protein is combined with a halide and a carbon source in a cultivation medium under conditions in which methyl formate is produced. The cell may genetically modified to express methyl formate synthase, methanol dehydrogenase and/or hydrolytic dehalogenase at levels higher than a cell of the same species that is not genetically modified. The methyl formate may be collected and used in a variety of applications. The halide may be chlorine, bromine or iodine.

Abstract: The invention relates to anti-sigma factors (“anti-sigmas”) that bind to sigma factors and block activation of transcription. Anti-sigmas and their cognate sigma factors provide a highly effective mechanism for regulating gene expression in genetic circuits.

Abstract: Methods for making synthetic gene clusters are described.

Abstract: The invention provides methods, materials and systems of regulating association between proteins of interest using light. In an aspect, the invention takes advantage of the ability of phytochromes to change conformation upon exposure to appropriate light conditions, and to bind in a conformation-dependent manner to cognate proteins called phytochrome-interacting factors. The invention comprises a method of regulating interaction between a first protein of interest and second protein within a cell by light. Such a method optionally comprises providing in the cell (1) a first protein construct which comprises the first protein, a phytochrome domain (PHD), and (2) providing in the cell a second protein construct which comprises the second protein and a phytochrome domain-interacting peptide (PIP) that can bind selectively to the Pfr state, but not to the Pr state, of the phytochrome domain.

Abstract: Disclosed is a process in which a recombinant organism, such as a yeast, expressing a heterologous S-adenosylmethionme (SAM)-dependent methyl halide transferase (MHT) protein is combined with a halide and a carbon source in a cultivation medium under conditions in which methyl formate is produced. The cell may genetically modified to express methyl formate synthase, methanol dehydrogenase and/or hydrolytic dehalogenase at levels higher than a cell of the same species that is not genetically modified. The methyl formate may be collected and used in a variety of applications. The halide may be chlorine, bromine or iodine.

Abstract: The invention provides methods, materials and systems of regulating association between proteins of interest using light. In an aspect, the invention takes advantage of the ability of phytochromes to change conformation upon exposure to appropriate light conditions, and to bind in a conformation-dependent manner to cognate proteins called phytochrome-interacting factors. The invention comprises a method of regulating interaction between a first protein of interest and second protein within a cell by light. Such a method optionally comprises providing in the cell (1) a first protein construct which comprises the first protein, a phytochrome domain (PHD), and (2) providing in the cell a second protein construct which comprises the second protein and a phytochrome domain-interacting peptide (PIP) that can bind selectively to the Pfr state, but not to the Pr state, of the phytochrome domain.

Abstract: The invention relates to systems and methods for production of compounds by yeast and other organisms. In one approach yeast engineered for production of a compound of commercial value is cultured together with a cellulosic bacteria, and the yeast uses a metabolic product produced by the bacteria as a carbon source. Methyl halides are an example of compounds that may be produced by this process. The invention also relates to production of organic compounds using genetically engineered organisms expressing a S-adenosylmethionine (SAM)-dependent methyl halide transferase. In one approach the organism, halides and a carbon source are incubated in a cultivation medium under conditions in which methyl halide is produced. The methyl halide may be collected and converted into non-halogenated organic molecules.

Abstract: The invention relates to a process for production of organic compounds using genetically engineered organisms expressing a S-adenosylmethionine (SAM)-dependent methyl halide transferase and, optionally modified at loci that affect flux through SAM metabolic pathways or affect intracellular halide levels. In one approach the organism, halides (chlorine, bromine and/or iodine); and a carbon source are incubated in a cultivation medium under conditions in which methyl halide is produced. The methyl halide may be collected and converted into non-halogenated organic molecules.

Abstract: The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying “structurally tolerant” residues of a polymer. Mutations of these, structurally tolerant residues are less likely to adversely affect desirable properties of a polymer sequence. The invention further provides improved methods for directed evolution wherein the structurally tolerant residues of a polymer are selectively mutated. Computer systems for implementing analytical methods of the invention are also provided.

Abstract: The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying “crossover locations” in a polymer. Crossovers at these locations are less likely to disrupt desirable properties of the protein, such as stability or functionality. The invention further provides improved methods for directed evolution wherein the polymer is selectively recombined at the identified “crossover locations”. Crossover disruption profiles can be used to identify preferred crossover locations. Structural domains of a biopolymer can also be identified and analyzed, and domains can be organized into schema. Schema disruption profiles can be calculated, for example based on conformational energy or interatomic distances, and these can be used to identify preferred or candidate crossover locations.

Abstract: The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying “crossover locations” in a polymer. Crossovers at these locations are less likely to disrupt desirable properties of the protein, such as stability or functionality. The invention further provides improved methods for directed evolution wherein the polymer is selectively recombined at the identified “crossover locations”. Crossover disruption profiles can be used to identify preferred crossover locations. Structural domains of a biopolymer can also be identified and analyzed, and domains can be organized into schema. Schema disruption profiles can be calculated, for example based on conformational energy or interatomic distances, and these can be used to identify preferred or candidate crossover locations.